Preheat oven to 375°F (190°C) and line a 12-cup muffin tin with paper liners.
Whisk almond milk and apple cider vinegar in a small bowl and let sit for 5 minutes to create vegan buttermilk.
In a large mixing bowl, whisk together the gluten-free flour, sugar, baking powder, baking soda, and salt.
Add the melted coconut oil and vanilla extract to the buttermilk mixture and whisk to combine.
Pour the wet ingredients into the dry ingredients and stir with a spatula until just combined.
Fold in 3/4 cup of the vegan chocolate chips.
Divide the batter evenly among the 12 muffin cups.
Top the batter with the remaining 1/4 cup of chocolate chips.
Bake for 20 to 22 minutes or until a toothpick inserted into the center comes out clean.
Cool in the pan for 5 minutes before transferring to a wire rack to cool completely.